The only con I know of is that the chambers and throats may have different dimensions so the rifles don't respond the same to a specific load.

My experience is with two 257 Roberts. One with a tight custom chamber shows signs of high pressure with some factory loads and some frequently listed hand loads. The other has a looser factory chamber and requires above book loads to reach book velocities. Neck sized cases fired in the factory barrel will not chamber or chamber with great difficulty in the custom barrel. Safe loads in the factory rifle are too hot for the custom rifle so I use different load data and different brands of brass in each to keep them straight. Otherwise I have to full-length resize the brass and settle for 100+ fps less velocity in the factory rifle.

"It is wise, though, to remember above all else: rifle, caliber, scope, and even bullets notwithstanding, the most important feature of successful big game hunting is to put that bullet in the correct place, the first time!" John Jobson